Rigging. Should bones be connected to one big mesh or to many meshes?
This is a matter of personal preference.

If the animation is generated procedurally, it is probably more efficient to make the rocks separate objects. Updating the single transformation of an object is much faster and less memory intense than manipulating a large number of vertices at once.

If the animation animated manually, then there is barely any difference. In Blender, the rig should mainly consist of an armature in which bones control the objects. The individual rocks can patented to the armatures bones or bound to them with a deforming armature modifier. Using the latter, there is no difference between a single or many objects (each with their own armature modifier). The animator is only supposed to interact wuth bones, the objects (less alone individual vertex groups) should be tucked away, so they don't get in the way while animating. The speed difference between a single armature modifier one one object with many vertex groups over many armature modifiers is neglible. Single objects parented to individual bones will have a slight speed advantage in case of a large number of rocks.